ArticleGenome biology2022
Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- A complete human pancreatic cancer genome.bioRxiv : the preprint server for biology · 2026Article
- Assessing current capabilities for incorporating lipidomics in multiomics data integration.Briefings in bioinformatics · 2026Review
- Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.Cell reports methods · 2026Article
- Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes.bioRxiv : the preprint server for biology · 2025Article
- Multi-platform framework for mapping somatic retrotransposition in human tissues.bioRxiv : the preprint server for biology · 2025Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data.Precision clinical medicine · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Genome assembly resources of genitourinary cancers for chromosomal aberration at the single nucleotide level.Scientific data · 2025Article
- A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.Life science alliance · 2024Article
- Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome.Genome biology · 2024Article
- The Application of Long-Read Sequencing to Cancer.Cancers · 2024Review
- Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.Genome biology · 2023Article
- A database of restriction maps to expand the utility of bacterial artificial chromosomes.GigaByte (Hong Kong, China) · 2023Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Towards accurate and reliable resolution of structural variants for clinical diagnosis.Genome biology · 2022Review
- Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.Nature biotechnology · 2021Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundThe use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but has never been explored in tumor-normal paired samples. Here, we provide the first demonstrated use of de novo assembled personalized genome as a reference for cancer mutation detection and quantifying the effects of the reference genomes on the accuracy of somatic mutation detection.
resultsWe generate de novo assemblies of the first tumor-normal paired genomes, both nuclear and mitochondrial, derived from the same individual with triple negative breast cancer. The personalized genome was chromosomal scale, haplotype phased, and annotated. We demonstrate that it provides individual specific haplotypes for complex regions and medically relevant genes. We illustrate that the personalized genome reference not only improves read alignments for both short-read and long-read sequencing data but also ameliorates the detection accuracy of somatic SNVs and SVs. We identify the equivalent somatic mutation calls between two genome references and uncover novel somatic mutations only when personalized genome assembly is used as a reference.
conclusionsOur findings demonstrate that use of a personalized genome with individual-specific haplotypes is essential for accurate detection of the full spectrum of somatic mutations in the paired tumor-normal samples. The unique resource and methodology established in this study will be beneficial to the development of precision oncology medicine not only for breast cancer, but also for other cancers.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.